Biology subjects

Cardozo Gizzi, A. M.

Publications and source records attributed to Cardozo Gizzi, A. M..

3 recordsLinked to original sources

bioRxiv2020

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during development

During development, naïve cells gradually acquire distinct cell fates, through sophisticated mechanisms of precise spatio-temporal gene regulation. Acquisition of cell fate is thought to rely on the specific interaction of remote cis-regulatory modules (e.g. enhancers, silencers) (CRM) and target promoters. However, the precise interplay between chromatin structure and gene expression is still unclear, particularly in single cells within multicellular developing organisms. Here we employ Hi-M, a single-cell spatial genomics approach, to systematically detect CRM-promoter looping interactions within topological associating domains (TADs) during Drosophila development. By comparing cis-regulatory loops in alternate cell types, we show that physical proximity does not necessarily instruct transcriptional states. Moreover, multi-way analyses revealed the existence of local interactions between multiple remote CRMs to form hubs. We found that loops and CRM hubs are established early during development, prior to the emergence of TADs. Moreover, CRM hubs are formed via the action of the pioneer transcription factor Zelda and precede transcriptional activation. Our approach offers a new perspective on the role of CRM-promoter interactions in defining transcriptional activation and repression states, as well as distinct cell types.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genomics↗

bioRxiv2018

Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms

Eukaryotic chromosomes are organized in multiple scales, from nucleosomes to chromosome territories. Recently, genome-wide methods identified an intermediate level of chromosome organization, topologically associating domains (TADs), that play key roles in transcriptional regulation. However, these methods cannot directly examine the interplay between transcriptional activation and chromosome organization while maintaining spatiotemporal information. Here, we present a multiplexed, sequential imaging approach (Hi-M) that permits the simultaneous detection of chromosome organization and transcription in single nuclei. We used Hi-M to study chromosome organization during the awakening of the zygotic genome in intact Drosophila embryos. By visualizing chromosome architecture and gene expression simultaneously in single nuclei, we were able to unveil the changes in 3D chromatin organization occurring upon transcriptional activation and homologous chromosome un-pairing. Excitingly, the ability of Hi-M to explore the multi-scale chromosome architecture in time and space will be key to understand the mechanisms and consequences of the 4D organization of the genome.

cell biology↗

bioRxiv2017

Single-cell absolute contact probability detection reveals that chromosomes are organized by modulated stochasticity

At the kilo- to mega-base pair scales, eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that associate to form nuclear compartments. Here, we combined high-content super-resolution microscopies with state-of-the-art DNA labeling methods to reveal the variability in the multiscale organization of the Drosophila genome. We found that association frequencies within TADs and between TAD borders are below ~10%, independently of TAD size, epigenetic state, or cell type. Critically, despite this large heterogeneity, we were able to visualize nanometer-sized epigenetic domains at the single-cell level. In addition, absolute contact frequencies within and between TADs were to a large extent defined by genomic distance, higher-order chromosome architecture, and epigenetic identity. We propose that TADs and compartments are organized by multiple, small frequency, yet specific interactions that are regulated by epigenetics and transcriptional state.

biophysics↗